Biology subjects

Latif, A.

Publications and source records attributed to Latif, A..

5 recordsLinked to original sources

bioRxiv2026

Computational and Structure-Guided E-Pharmacophore-Based Virtual Screening for the Identification of Novel NEK2 Kinase Inhibitors as Potential Anticancer Agents

Cancer is a serious public health problem, and is becoming more common, with a projected increase in deaths and more than 25 million new cases in coming decades. A number of molecular mechanisms are involved in the tumoral process, with one of them, never in mitosis A-related kinase 2 (NEK2), a serine/threonine protein kinase, being a frequent target of amplification in various malignancies that is responsible for chromosomal instability, aneuploidy and activation of several oncogenic pathways. Available kinase inhibitors are not yet optimized in terms of their pharmacokinetic properties for clinical use, and current therapies, such as chemotherapeutic agents or immunotherapies are often limited by their resistance. In silico methods represent an effective tool to search for novel potent inhibitors, before testing in animals, with time constraints and limited resources. To find new inhibitors of NEK2, we used E pharmacophore-based modeling and structure based virtual screening in this study. NEK2 was chosen as the target for therapeutic intervention and an energy optimized pharmacophore model was employed to screen the Enamine REAL library of millions of compounds. Pharmacodynamic and Pharmacokinetic properties of the Top hits were tested using ADMET profiling. These were further screened using molecular docking (standard precision and extra precision) and virtual screening to obtain three lead compounds 1, 2, and 3 which have docking score of -7.414, -8.037 and -7.562 respectively. MM-GBSA calculations were used to estimate the binding free energies for these complexes, which were determined to be -54.92, -54.18 and -49.23 kcal/mol. Lastly, 100 ns molecular dynamics simulations have been run to evaluate complex stability in dynamic situations. The overall results of the MD showed the overall stability of the NEK2-ligand complexes, and thus these three compounds are promising NEK2 inhibitor candidates and could be further validated in vitro and in vivo for clinical application. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/742111v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@14e9cfeorg.highwire.dtl.DTLVardef@24ec78org.highwire.dtl.DTLVardef@20be75org.highwire.dtl.DTLVardef@1b80c02_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

An Organotypic Oral Squamous Cell Carcinoma Model Recapitulates Epithelial-Stromal Complexity at Single-cell Resolution and Reveals Matrix-derived Signalling as a Therapeutic Target.

Three-dimensional (3D) organotypic cultures recapitulate key structural features of oral tumours and provide controlled, ethical, and reproducible research platforms. However, their ability to faithfully recapitulate in vivo tissue composition and their translational relevance require rigorous validation. Here, we characterised a head and neck squamous cell carcinoma (HNSCC) model using single-cell RNA sequencing to assess maturation, cellular heterogeneity, functionality, and inter- and intra-tissue interactions within epithelial and stromal compartments. The epithelial layer of the model differentiated into populations closely resembling the tissue of tumour origin, including dividing and precursor cells, heterogeneous basal layer, suprabasal cells, and metabolically specialised populations. All epithelial lineages emerged from proliferative progenitors, driven by dynamic transcription factor programmes. The collagen-rich stroma contained functionally diverse fibroblasts reflecting the heterogeneity of cancer-associated fibroblasts in vivo, including dividing, matrix-producing, immune-responsive, and tumour-like populations. Importantly, extensive epithelial-stromal communication networks developed, essential for cancer epithelium maintenance and tumour microenvironment regulation. Matrix-derived signals, particularly fibronectin, osteopontin, and laminins, constituted dominant inputs to CD44-expressing cancer cells and are associated with patient survival in HNSCC, highlighting potential therapeutic targets. Overall, this organotypic HNSCC model exhibits high functional fidelity, captures key tumour elements relevant for therapy and resistance and brings confidence in non-animal drug testing.

cancer biology↗

bioRxiv2022

Invasion and Secondary Site Colonization as a function of In vitro Primary Tumor Matrix Stiffness

Increased breast tissue stiffness is correlated with breast cancer risk and invasive cancer progression. However, its role in promoting bone metastasis, which shares a large burden of breast cancer deaths, has not yet been understood. To better understand the cause-effect relationship of tissue stiffness on breast cancers metastatic potential, we fabricated three-dimensional (3D) models to mimic breast and bone tissue in vitro. Based on our previous work, we used alginate-based hydrogels allowing precise control over stiffness and composition of extracellular breast tissue matrix; and 3D printed poly-caprolactone (PCL)-composite scaffolds to mimic the bone. The latter were further modified by promoting bone-ECM deposition using Saos-2 cells. After a decellularization step, PCL scaffolds were assembled with alginate-gelatin hydrogels and a novel breast-to-bone in vitro model was established. It was observed that increased stiffness of hydrogel resulted in higher migration and invasion capacity of MDA-MB 231 cells. Additionally, PTHrP and IL-6 expression, both of which are implicated in bone metastasis, were higher when cells from stiff hydrogels were cultured in bone/PCL scaffolds. These breast-to-bone in vitro models pose as a novel non-animal technology to pave the way for incorporating important tissue microenvironmental factors of the disease physiology (e.g. tissue stiffness) and emerge as promising future platforms for monitoring metastatic disease phenotypes and therapeutic efficacy.

bioengineering↗

bioRxiv2022

Monocarboxylate Transporters are Involved in Extracellular Matrix Remodelling in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a five-year survival rate of <8%. PDAC is characterised by desmoplasia with abundant extracellular matrix (ECM) rendering current therapies ineffective. Monocarboxylate transporters (MCTs) are key regulators of cellular metabolism and are upregulated in different cancers, however their role in PDAC desmoplasia is little understood. Here, we investigated MCT and ECM gene expression in primary PDAC patient biopsies using RNA-sequencing data obtained from Gene Expression Omnibus. We generated a hypernetwork model from these data to investigate whether a causal relationship exists between MCTs and ECMs. Our analysis of stromal and epithelial tissues (n=189) revealed 9 differentially expressed MCTs, including upregulation of SLC16A2/6/10 and the non-coding SLC16A1-AS1, and 502 ECMs including collagens, laminins, and ECM remodelling enzymes (false discovery rate<0.05). Causal hypernetwork analysis demonstrated a bidirectional relationship between MCTs and ECMs; 4 MCT and 255 ECM-related transcripts correlated with 90% of differentially expressed ECMs (n=376) and MCTs (n=7), respectively. The hypernetwork model was robust, established by two independent approaches involving iterated sampling and silencing of indirect interactions in the network. This transcriptomic analysis highlights the role of MCTs in PDAC desmoplasia via associations with ECMs, opening novel treatment pathways to improve patient survival. Simple SummaryMonocarboxylate transporters (MCTs) carry a variety of substrates with MCT1-4 being well characterised and involved in proton-coupled transport of monocarboxylates (such as lactate) which can be used as metabolic fuel for cancer cells. Increased acidity of tumour microenvironment via MCTs favours remodelling of extracellular matrix (ECM) leading to desmoplasia associated with tumour metastasis and poor patient outcomes. Although MCT1-2/4 are upregulated in several cancers, their expression and role in pancreatic ductal adenocarcinoma desmoplasia is little understood. Here, we aimed to understand the role of MCTs in desmoplasia through their associations with ECM components. Our analysis using hypernetworks showed the presence of bidirectional associations of MCTs and ECMs, suggesting the presence of a causal relationship and the need to further investigate their functional associations. It confirms the role of MCTs in desmoplasia highlighting their importance as therapeutic targets alone or in combination with key ECM components to potentially improve patient outcomes.

cancer biology↗

bioRxiv2020

Toll-like receptor 4 is activated by platinum and contributes to cisplatin-induced ototoxicity

Toll-like receptor 4 (TLR4) is famous for recognizing the bacterial endotoxin lipopolysaccharide (LPS) as its canonical ligand. TLR4 is also activated by other classes of agonist including some Group 9/10 transition metals. Roles for these non-canonical ligands in pathobiology mostly remain obscure, though TLR4 interactions with metals can mediate immune hypersensitivity reactions. In this work, we tested whether TLR4 can be activated by the Group 10 transition metal, platinum. We demonstrated that in the presence of TLR4, platinum activates pathways downstream of TLR4 to a similar extent as the known TLR4 agonists LPS and nickel. Platinum is the active moiety in cisplatin, a very potent and invaluable chemotherapeutic used to treat solid tumors in childhood cancer patients. Unfortunately, cisplatin use is limited due to an adverse effect of permanent hearing loss (cisplatin-induced ototoxicity, CIO). Herein, we demonstrated that cisplatin also activates TLR4, prompting the hypothesis that TLR4 mediates aspects of CIO. Cisplatin activation of TLR4 was independent of the TLR4 co-receptors CD14 and MD-2, which is consistent with TLR4 signaling elicited by transition metals. We found that TLR4 is required for cisplatin-induced inflammatory, oxidative and apoptotic responses in an ear outer hair cell line and for hair cell damage in vivo. Thus, TLR4 is a promising therapeutic target to mitigate CIO. We additionally identify a TLR4 small molecule inhibitor able to curtail cisplatin toxicity in vitro. Further work is warranted towards inhibiting TLR4 as a route to mitigating this adverse outcome of childhood cancer treatment.Significance Statement This work identifies platinum, and its derivative cisplatin, as new agonists for TLR4. TLR4 contributes to cisplatin-induced hair cell death in vitro and in vivo. Genetic and small molecule inhibition of TLR4 identify this receptor as a druggable therapeutic target with promise to curtail cisplatin-induced ototoxicity, a devastating side-effect of an otherwise invaluable chemotherapeutic tool.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pharmacology and toxicology↗